Auryn simulator

Simulator for spiking neural networks with synaptic plasticity

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examples:sim_coba_benchmark [2014/09/12 10:46] – Updates tutorial with new syntax for example. zenkeexamples:sim_coba_benchmark [2015/06/01 17:58] – zenke
Line 28: Line 28:
  
 {{ :examples:coba_ras.png?300 |}} {{ :examples:coba_ras.png?300 |}}
-This figure shows the rasterplot of the spiking activity of the excitatory population written to ''/tmp/coba.0.e.ras''.+This figure shows the raster plot of the spiking activity of the excitatory population written to ''/tmp/coba.0.e.ras''.
  
  
Line 43: Line 43:
 neurons_i->random_mem(-70e-3,10e-3); neurons_i->random_mem(-70e-3,10e-3);
 </code> </code>
-This part instatiates two groups of neurons of type [[TIFGroup]] which corresponds to the conductance based model with exponentially decaying PSCs and an absolute refractoriness of 5ms. The ''random_mem'' methods randomize the initial membrane potentials with a Gaussian (mean=-70mV and standard deviation 10e-3mV).+This part instatiates two groups of neurons of type [[TIFGroup]] which corresponds to the conductance based model with exponentially decaying PSCs and an absolute refractoriness of 5ms. The ''random_mem'' methods randomize the initial membrane potentials with a Gaussian (mean=-70mV and standard deviation 10mV).
  
  
Line 80: Line 80:
  
 ===== The full program ===== ===== The full program =====
 +**Note** you might find a more recent version of this code in the ''auryn/examples'' directory.
 +
 <code c++> <code c++>
 /*  /* 
Line 119: Line 121:
 #include "WeightSumMonitor.h" #include "WeightSumMonitor.h"
 #include "SpikeMonitor.h" #include "SpikeMonitor.h"
 +#include "DelayedSpikeMonitor.h"
 #include "StateMonitor.h" #include "StateMonitor.h"
 #include "RateChecker.h" #include "RateChecker.h"
Line 139: Line 142:
  string msg;  string msg;
  
- double w = 0.4; + double w = 0.4; // [g_leak] 
- double wi = 5.1;+ double wi = 5.1; // [g_leak]
  
  
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  NeuronID ni = 800;  NeuronID ni = 800;
  
- bool prime = false; 
  bool fast = false;  bool fast = false;
  
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             ("help", "produce help message")             ("help", "produce help message")
             ("simtime", po::value<double>(), "simulation time")             ("simtime", po::value<double>(), "simulation time")
-            ("prime", "switch input modalities") 
             ("fast", "turns off most monitoring to reduce IO")             ("fast", "turns off most monitoring to reduce IO")
             ("dir", po::value<string>(), "load/save directory")             ("dir", po::value<string>(), "load/save directory")
Line 182: Line 183:
         if (vm.count("simtime")) {         if (vm.count("simtime")) {
  simtime = vm["simtime"].as<double>();  simtime = vm["simtime"].as<double>();
-        }  
- 
-        if (vm.count("prime")) { 
- prime = true; 
         }          } 
  
Line 237: Line 234:
  // END Global stuff  // END Global stuff
  
- 
- // double primetime = 10; 
  logger->msg("Setting up neuron groups ...",PROGRESS,true);  logger->msg("Setting up neuron groups ...",PROGRESS,true);
  
Line 244: Line 239:
  TIFGroup * neurons_i = new TIFGroup( ni);  TIFGroup * neurons_i = new TIFGroup( ni);
  
- neurons_e->random_mem(-70e-3,10e-3); + neurons_e->set_state("bg_current",2e-2); // corresponding to 200pF for C=200pF and tau=20ms 
- neurons_i->random_mem(-70e-3,10e-3);+ neurons_i->set_state("bg_current",2e-2);
  
  
Line 265: Line 260:
  = new SparseConnection( neurons_i,neurons_i,wi,sparseness,GABA);  = new SparseConnection( neurons_i,neurons_i,wi,sparseness,GABA);
  
- if ( prime ) {  + if ( !fwmat_ee.empty() ) con_ee->load_from_complete_file(fwmat_ee); 
- msg = "Setting up external input ..."; + if ( !fwmat_ei.empty() ) con_ei->load_from_complete_file(fwmat_ei); 
- logger->msg(msg,PROGRESS,true); + if ( !fwmat_ie.empty() ) con_ie->load_from_complete_file(fwmat_ie); 
- + if ( !fwmat_ii.empty() ) con_ii->load_from_complete_file(fwmat_ii);
- PoissonGroup * poisson= new PoissonGroup(200,10); +
- poisson->seed(132341);  +
- // this will give the same seed on each rank, +
- // but since the group should be locked to a single +
- // rank we do not care. +
- +
- SparseConnection * con_ext_e = new SparseConnection(poisson,neurons_e,1,sparseness/2,GLUT); +
- SparseConnection * con_ext_i = new SparseConnection(poisson,neurons_i,1,sparseness/2,GLUT); +
- +
- } else { +
- oss.str(""); +
- oss << dir << "/save"; +
- sys->load_network_state(oss.str()); +
- } +
- +
- if ( !fwmat_ee.empty() ) con_ee->load_from_file(fwmat_ee); +
- if ( !fwmat_ei.empty() ) con_ei->load_from_file(fwmat_ei); +
- if ( !fwmat_ie.empty() ) con_ie->load_from_file(fwmat_ie); +
- if ( !fwmat_ii.empty() ) con_ii->load_from_file(fwmat_ii); +
- +
- +
- // pruning here impairs performance -- probably due to cache poisoning +
- con_ee->prune(); +
- con_ei->prune(); +
- con_ie->prune(); +
- con_ii->prune();+
  
  
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  filename << outputfile << "e.ras";  filename << outputfile << "e.ras";
  SpikeMonitor * smon_e = new SpikeMonitor( neurons_e, filename.str().c_str() );  SpikeMonitor * smon_e = new SpikeMonitor( neurons_e, filename.str().c_str() );
 +
 + // filename.str("");
 + // filename.clear();
 + // filename << outputfile << "e.dras";
 + // DelayedSpikeMonitor * dsmon_e = new DelayedSpikeMonitor( neurons_e, filename.str().c_str() );
  
  filename.str("");  filename.str("");
Line 312: Line 286:
  filename.str("");  filename.str("");
  filename << outputfile << "e.mem";  filename << outputfile << "e.mem";
- StateMonitor * smon_mem = new StateMonitor( neurons_e, 3, "mem", filename.str() ); + StateMonitor * smon_mem = new StateMonitor( neurons_e, 7, "mem", filename.str() ,dt ); 
   
  filename.str("");  filename.str("");
  filename << outputfile << "e.ampa";  filename << outputfile << "e.ampa";
- StateMonitor * smon_ampa = new StateMonitor( neurons_e, 3, "g_ampa", filename.str() );+ StateMonitor * smon_ampa = new StateMonitor( neurons_e, 7, "g_ampa", filename.str() );
  
  filename.str("");  filename.str("");
  filename << outputfile << "e.gaba";  filename << outputfile << "e.gaba";
- StateMonitor * smon_gaba = new StateMonitor( neurons_e, 3, "g_gaba", filename.str() );+ StateMonitor * smon_gaba = new StateMonitor( neurons_e, 7, "g_gaba", filename.str() );
  }  }
  
Line 335: Line 309:
  if (!sys->run(simtime,true))   if (!sys->run(simtime,true)) 
  errcode = 1;  errcode = 1;
- 
- if ( prime ) {  
- oss.str(""); 
- oss << dir << "/save"; 
- sys->save_network_state(oss.str()); 
- } 
  
  logger->msg("Freeing ..." ,PROGRESS,true);  logger->msg("Freeing ..." ,PROGRESS,true);
examples/sim_coba_benchmark.txt · Last modified: 2016/07/05 23:40 by zenke